Interpretive Summary: Copy number variations (CNVs) are a main source of genomic structural variation underlying animal evolution and production traits. Using bioinformatic tools and whole genome analysis, we identified 470 CNV regions in Chinese domesticated bulls; their effects on gene activities were also examined. Some of the variations were linked with gene activity and some were linked with cattle body measurements. The results advanced our understanding of CNVs as an important population genomic variation in different Chinese cattle breeds. This study provides a highly valuable resource for Chinese cattle evolution and breeding research.

Technical Abstract:
Copy number variations (CNVs) are a main source of genomic structural variations underlying animal evolution and production traits. Here, we describe a genome-wide analysis of CNVs in Chinese domesticated bulls and examination of their effects on gene expression and cattle growth traits. We identified 470 copy number variable regions (CNVRs), covering 2.13 % of the bovine genome in taurine/indicine cattle, together with 127 in yak and 148 in buffalo. We discovered 605 integrated CNVRs, with more “loss” events than both “gain” and “both” ones, and clearly clustered them into three cattle groups. Interestingly, we confirmed their uneven distributions across chromosomes, and the divided differences of mitochondrion DNA copy number (gain: taurine/indicine, loss: yak and buffalo). Furthermore, we confirmed that approximately 26.6% (125/470) and 67.2% (316/470) CNVRs span cattle genes and quantitative trait loci (QTLs), respectively. Finally, we chose quantitative PCR–confirmed CNVRs for detailed functional analysis. We demonstrated that CNVR14 had significantly negative effects on expression of PLA2G2D gene, and both CNVR14 and CNVR237 were associated with body measurements in Chinese cattle, suggesting their key effects on gene expression and cattle traits. The results advanced our understanding of CNV as an important population genomic variation in taurine/indicine, yak, and buffalo. This study provides a highly valuable resource for Chinese cattle evolution and breeding research.